[BioC] Problems with affycomp - quantile.default

[Markus Schmidberger]

Hi Jim,

thanks a lot, now it works.
But what is wrong by reading the phenodata-File

 > pd95<-read.AnnotatedDataFrame(filename="spikein_pdata.txt", 
header=TRUE, row.names="filename", sep=" ")

 > colnames(pData(pd95))
 [1] "X37777_at" "X684_at"   "X1597_at"  "X38734_at" "X39058_at" "X36311_at"
 [7] "X36889_at" "X1024_at"  "X36202_at" "X36085_at" "X40322_at" "X407_at" 
[13] "X1091_at"  "X1708_at"  "X33818_at" "X546_at" 

Attached the pdata-File from the affycompII website 
(http://affycomp.biostat.jhsph.edu/)
(set="\t" also does not work)

Thanks
Markus


James W. MacDonald schrieb:
> Are you sure you have the correct phenoData? What do you get from
>
> colnames(pData(eset))?
>
> You should get this:
>
> > colnames(pData(eset))
>  [1] "37777_at" "684_at"   "1597_at"  "38734_at" "39058_at" "36311_at"
>  [7] "36889_at" "1024_at"  "36202_at" "36085_at" "40322_at" "407_at"
> [13] "1091_at"  "1708_at"  "33818_at" "546_at"
>
> If you don't, you have the incorrect phenoData, and you should use
>
> pd <- as(data(spikein.phenodata), "AnnotatedDataFrame")
>
> Best,
>
> Jim
>
>
>
> Markus Schmidberger wrote:
>> Hello,
>>
>> Phenodata do not help. I changed my code to this:
>>
>> library(affy)
>> library(affycomp)
>> pathRawData <- "~/Microarray/hgu95a-spikein/rawdata"
>> pathPhenoData <- "~/Microarray/hgu95a-spikein/spikein_pdata.txt"
>> celFile <- list.celfiles(path=pathRawData,full.names=TRUE);
>> pd<-read.AnnotatedDataFrame(filename=pathPhenoData, header=TRUE, 
>> row.names="filename", sep=" ")
>> affyBatch <- ReadAffy(filenames=celFile, phenoData=pd);
>> eset <- rma(affyBatch)
>> assessFC(eset,method.name="RMA")
>>
>> and I still have the same error:
>> Fehler in quantile.default(m[-spikeindex], prob = probs) :
>>         missing values and NaN's not allowed if 'na.rm' is FALSE
>>
>> (same error with the hgu133 dataset)
>>
>> What I have to change?
>>
>> Thanks,
>> Markus
>>
>> James MacDonald schrieb:
>>> Hi Markus,
>>>
>>> Markus Schmidberger wrote:
>>>> Hello,
>>>>
>>>> I want to do some comparison with affycomp and use the affycompII 
>>>> data. This is my code
>>>>
>>>> library(affy)
>>>> library("affycomp")
>>>> path <- "/Microarray/hgu95a-spikein/rawdata"
>>>> celFile <- list.celfiles(path=path,full.names=TRUE);
>>>> affyBatch <- ReadAffy(filenames=celFile);
>>>> eset1 <- rma(affyBatch)
>>>> assessFC(eset1,method.name="RMA.2")
>>>>
>>>> and I get the ERROR:
>>>> Fehler in quantile.default(m[-spikeindex], prob = probs) :
>>>>         missing values and NaN's not allowed if 'na.rm' is FALSE
>>> If you look at the code for assessFC(), you will see that the 
>>> spikeindex comes from the phenoData slot of the ExpressionSet object 
>>> (in particular the genenames column, which I assume lists the 
>>> probesets that were spiked in). If you don't have this information 
>>> in your phenoData slot, then assessFC() won't work, and I assume 
>>> this to be true of the other assessXX() functions as well.
>>>
>>> The phenoData can be accessed using data(spikein.phenodata). 
>>> Unfortunately this is an old-style phenoData object instead of an 
>>> AnnotatedDataFrame, so you have to update first.
>>>
>>> pd <- data(spikein.phenodata)
>>> pd <- as(pd, "AnnotatedDataFrame")
>>> ## you will see warnings here that I think you can ignore
>>> affyBatch <- ReadAffy(filenames=celFile, phenoData=pd)
>>>
>>> should get you going.
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>>> How to fix this?
>>>>
>>>> R version 2.5.0 (2007-04-23)
>>>> i686-pc-linux-gnu
>>>> locale:
>>>> LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C 
>>>>
>>>> attached base packages:
>>>> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     
>>>> "datasets"
>>>> [7] "methods"   "base"    other attached packages:
>>>> hgu95acdf  affycomp      affy    affyio   Biobase
>>>>  "1.16.0"  "1.12.0"  "1.14.1"   "1.4.0"  "1.14.0"
>>>>
>>>> Thanks,
>>>> Markus
>>>>
>>
>>
>


-- 
Dipl.-Tech. Math. Markus Schmidberger

Ludwig-Maximilians-Universität München
IBE - Institut für medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
URL: http://ibe.web.med.uni-muenchen.de 
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
Tel: +49 (089) 7095 - 4599

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